Incognito is not recommended for a variety of reasons. It functions by blanking parts of your console’s PRODINFO, which is console-unique data that your console requires to boot. If Incognito goes wrong, malfunctions, or if you lose the backup, it can result in damage to the functionality of your console, up to and including a brick and never being able to go online again.
Part of the way Incognito functions is by forcing your console to send "invalid data" when connecting to Nintendo servers, which at the time reject such invalid connections. If Nintendo wanted to, they could simply set their servers to receive these connections, and then everyone and anyone relying on Incognito will be sending all of their telemetry to Nintendo instantly.
The other issue with Incognito is that what it does delete, is (to speak simply) significantly short of everything that it should delete to have the functionality it claims to have. This is roughly equivalent to blanking out your street address when showing your driver's license to the police, but showing your full legal name.
As of Atmosphere 0.12.0, a virtual PRODINFO blanking feature is included, which is safer than Incognito as the relevant data is redirected not deleted, but this method of protection is still not a viable replacement for 90DNS.
(Thanks to Discord user noirscape#6666 on the Nintendo Homebrew Discord server for the explanation of why Incognito is bad, also denn and meme)
